Our approach in identifying candidate genes for ischaemic stroke involved the selection and genotyping of common polymorphisms of genes which may influence one of the major risk factors for stroke. Materials and Methods. DNA from Caucasian populations of control subjects and stroke patients was made available for PCR and subsequent genotyping, which included RFLP analysis, DASH and microsatellite analysis. Our chosen genes included the GNbeta3 gene (the C825T polymorphism), the p22PHOX gene the C242T and A640G polymorphisms) and the ERalpha gene (the PvuII, XbaI SNPs and TA dinucleotide tandem repeat polymorphism). Statistical tests were then used to determine whether genotype/allele frequencies were significantly different in case-control analyses. Where appropriate (multiple markers investigated), haplotype analysis was also performed to test for linkage disequilibrium. In addition, we collaborated with deCode Genetics (Iceland) on the genotyping of 5 novel SNPs and 2 microsatellite polymorphisms on an Icelandic stroke population as well as our own Scottish stroke patients. Results. From our results, there were no positive associations revealed with any of the three candidate genes. However, through our collaboration with deCode Genetics, two polymorphisms (1 SNP and 1 microsatellite) were found to be significantly associated with ischaemic stroke in both Icelandic and Scottish patient populations. Haplotype analysis of these two markers also revealed a significant difference between cases and controls. Discussion. The future success of population association studies of complex disorders will require replication of both negative and positive findings in geographically/ethnically different populations. Identification of the potential "stroke" gene on 5q12 may lead to identification of novel therapeutic targets.